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comparison cuffcompare_wrapper.xml @ 2:a5674ddf2ad7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:37:50 -0500
parents 6d8ab54229a0
children 5aac9b9d6f2a
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1:6d8ab54229a0 2:a5674ddf2ad7
1 <tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0"> 1 <tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0">
2 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description> 2 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
7 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <version_command>cuffcompare 2>&amp;1 | head -n 1</version_command> 8 <version_command>cuffcompare 2>&amp;1 | head -n 1</version_command>
9 <command interpreter="python"> 9 <command>
10 cuffcompare_wrapper.py 10 python '$__tool_directory__/cuffcompare_wrapper.py'
11 ## Use annotation reference? 11 ## Use annotation reference?
12 #if $annotation.use_ref_annotation == "Yes": 12 #if $annotation.use_ref_annotation == "Yes":
13 -r $annotation.reference_annotation 13 -r '$annotation.reference_annotation'
14 #if $annotation.ignore_nonoverlapping_reference: 14 #if $annotation.ignore_nonoverlapping_reference:
15 -R 15 -R
16 #end if 16 #end if
17 #if $annotation.ignore_nonoverlapping_transfrags: 17 #if $annotation.ignore_nonoverlapping_transfrags:
18 -Q 18 -Q
22 22
23 ## Use sequence data? 23 ## Use sequence data?
24 #if $seq_data.use_seq_data == "Yes": 24 #if $seq_data.use_seq_data == "Yes":
25 -s 25 -s
26 #if $seq_data.seq_source.index_source == "history": 26 #if $seq_data.seq_source.index_source == "history":
27 --ref_file=$seq_data.seq_source.ref_file 27 --ref_file '$seq_data.seq_source.ref_file'
28 #else: 28 #else:
29 --index=${seq_data.seq_source.index.fields.path} 29 --index '${seq_data.seq_source.index.fields.path}'
30 #end if 30 #end if
31 #end if 31 #end if
32 32
33 $discard_single_exon 33 $discard_single_exon
34 34
38 #if $discard_intron_redundant_transfrags: 38 #if $discard_intron_redundant_transfrags:
39 -F 39 -F
40 #end if 40 #end if
41 41
42 ## Outputs. 42 ## Outputs.
43 --combined-transcripts=${transcripts_combined} 43 --combined-transcripts '${transcripts_combined}'
44 44
45 @CUFFLINKS_GTF_INPUTS@ 45 @CUFFLINKS_GTF_INPUTS@
46 </command> 46 </command>
47 <inputs> 47 <inputs>
48 <expand macro="cufflinks_gtf_inputs" /> 48 <expand macro="cufflinks_gtf_inputs" />